Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 5483-YLR022C_NumOfGenes_2 | YLR022C | SDO1 | guanine nucleotide exchange factor SDO1 | Guanine nucleotide exchange factor (GEF) for Ria1p; essential protein involved in ribosome maturation; with Ria1p, promotes release of Tif6p from 60S ribosomal subunits in the cytoplasm so that they can assemble with 40S subunits to generate mature ribosomes; ortholog of the human protein (SBDS) responsible for autosomal recessive Shwachman-Bodian-Diamond Syndrome; highly conserved across archaea and eukaryotes | Core | NA | NA | NA |
| 5484-YLR023C | YLR023C | IZH3 | NA | Membrane protein involved in zinc ion homeostasis; member of the four-protein IZH family, expression induced by zinc deficiency; deletion reduces sensitivity to elevated zinc and shortens lag phase, overexpression reduces Zap1p activity | Core | NA | NA | NA |
| 5485-YLR024C | YLR024C | UBR2 | putative ubiquitin-protein ligase UBR2 | Cytoplasmic ubiquitin-protein ligase (E3); component of the Mub1p-Ubr2p-Rad6p ubiquitin ligase complex required for the ubiquitination and degradation of Rpn4p; mediates formation of the ternary complex | Core | NA | NA | NA |
| 5486-YLR025W | YLR025W | SNF7 | ESCRT-III subunit protein SNF7|VPL5|RNS4|VPS32|DID1 | One of four subunits of the ESCRT-III complex; involved in the sorting of transmembrane proteins into the multivesicular body (MVB) pathway; recruited from the cytoplasm to endosomal membranes; ESCRT-III stands for endosomal sorting complex required for transport III | Core | NA | NA | NA |
| 5487-YLR026C | YLR026C | SED5 | t-SNARE syntaxin | cis-Golgi t-SNARE syntaxin; required for vesicular transport between the ER and the Golgi complex; binds at least 9 SNARE proteins | Core | NA | NA | NA |
| 5488-YLR027C | YLR027C | AAT2 | aspartate transaminase AAT2|ASP5 | Cytosolic aspartate aminotransferase involved in nitrogen metabolism; localizes to peroxisomes in oleate-grown cells | Core | NA | NA | NA |
| 5489-YLR028C | YLR028C | ADE16 | bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase ADE16 | Enzyme of 'de novo' purine biosynthesis; contains both 5-aminoimidazole-4-carboxamide ribonucleotide transformylase and inosine monophosphate cyclohydrolase activities; ADE16 has a paralog, ADE17, that arose from the whole genome duplication; ade16 ade17 mutants require adenine and histidine | Core | NA | NA | NA |
| 5490-YLR029C | YLR029C | RPL15A | eL15|ribosomal 60S subunit protein L15A|L15e|rp15R|YL10|L15A|L13A|RPL10A | Ribosomal 60S subunit protein L15A; binds to 5.8 S rRNA; homologous to mammalian ribosomal protein L15, no bacterial homolog; RPL15A has a paralog, RPL15B, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5491-YLR030W | YLR030W | NA | NA | Putative protein of unknown function; S288C contains an in-frame stop codon between ORFs YLR030W and YLR031W | Core | NA | NA | NA |
| 5492-YLR031W | YLR031W | NA | NA | Putative protein of unknown function; S288C contains an in-frame stop codon between ORFs YLR030W and YLR031W; YLR031W has a paralog, YMR124W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5493-YLR032W | YLR032W | RAD5 | DNA helicase RAD5|SNM2|REV2 | DNA helicase/Ubiquitin ligase; involved in error-free DNA damage tolerance (DDT), replication fork regression during postreplication repair by template switching, error-prone translesion synthesis; promotes synthesis of free and PCNA-bound polyubiquitin chains by Ubc13p-Mms2p; forms nuclear foci upon DNA replication stress; associates with native telomeres, cooperates with homologous recombination in senescent cells; human homolog HLTF can complement yeast null mutant | Core | NA | NA | NA |
| 5494-YLR033W | YLR033W | RSC58 | NA | Component of the RSC chromatin remodeling complex; RSC functions in transcriptional regulation and elongation, chromosome stability, and establishing sister chromatid cohesion; involved in telomere maintenance | Core | NA | NA | NA |
| 5495-YLR034C | YLR034C | SMF3 | putative divalent metal ion transporter SMF3 | Putative divalent metal ion transporter involved in iron homeostasis; transcriptionally regulated by metal ions; member of the Nramp family of metal transport proteins; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5496-YLR035C | YLR035C | MLH2 | mismatch repair protein MLH2 | Protein involved in mismatch repair and meiotic recombination; only certain frameshift intermediates are mismatch repair substrates; forms a complex with Mlh1p | Core | NA | NA | NA |
| 5497-YLR036C_NumOfGenes_2 | YLR036C | NA | NA | Putative protein predicted to have transmembrane domains; interacts with HSP90 by yeast two-hybrid analysis; YLR036C is not an essential protein | Core | NA | NA | NA |